Background and purpose To compare positional and volumetric differences of planning target volumes (PTVs) based on axial three-dimensional CT (3DCT) and four-dimensional CT (4DCT) for the primary tumor of non-small cell lung cancer (NSCLC). Materials and methods Twenty-eight patients with NSCLC underwent 3DCT and 4DCT scans of the thorax during normal free breathing. PTV vector was defined on 3DCT using the individual tumor motion vector measured by 4DCT accounting for tumor motion; PTV 4D was defined on all phases of 4DCT images. In addition, a 7 mm margin for microscopic disease and a 3 mm setup margin were used for above PTVs, respectively. The differences in target position, volume and coverage between PTV vector and PTV 4D were evaluated for tumors in different lobes, respectively. Results The median motion vector for tumors located in the upper lobe (group A) and in the middle lower lobe (group B) was 2.8 and 7 mm, respectively. The mean centroid shifts between PTV vector and PTV 4D in the LR, AP and CC directions for group A and B were close to zero. The median size ratio of PTV 4D to PTV vector was 0.75 and 0.52 for group A and B. The motion vector showed a significant correlation to the ratio of PTV 4D to PTV vector for group A and B ( p = 0.008 and 0.003). The median DI of PTV vector in PTV 4D was 69.19% for group A and 51.60% for group B. The median DI of PTV 4D in PTV vector was 98.99% for group A and 99.94% for group B. Conclusion It is necessary to expand the internal margin isotropically in a single direction for 3DCT treatment planning due to the uncertainty of the 3DCT-based target position. The 3DCT-based PTV using individual margins provides a good coverage of the 4DCT-based PTV, meanwhile encompasses relatively large normal tissues, especially for middle and lower lobe tumors. We should be cautious about the use of the individual PTV derived from 3DCT in treatment planning.